Sciencemadness Discussion Board
Not logged in [Login - Register]
Go To Bottom

Printable Version  
 Pages:  1    3  ..  5
Author: Subject: help with mechanisms
cheeseandbaloney
Harmless
*




Posts: 21
Registered: 4-4-2008
Member Is Offline


[*] posted on 12-8-2010 at 15:40
help with mechanisms


I wasn't sure where to put this, so I thought I'd ask here first. For any of the organic chemists out there I would greatly appreciate help with some mechanisms. One example is after addition of dichlorocarbene across the diene in cyclopentene the usual product is obtained. But the subsequent reaction that causes the ring to expand into the product 1,6-dichlorocyclohexene is where I am stuck. I feel a little sloppy on carbon-carbon bond breaking and ring expansion mechanisms. I feel that I don't fully grasp the rules on electron transfers during C-C breakage. Also, if anyone can point me in the right direction for pages on mechanisms like these that could help give me a better and deeper understanding of these 'rules' would be appreciated.

p.s. - This is all for pure curiosity and the drive to learn organic chemistry. I am not in school so I do not have the privilege of asking a professor, so I turn to you. I've looked in my books, but the one I have with the question was bought used online and doesn't have the solutions manual. I've looked online but the only link available to download the solutions manual .pdf is broken.
View user's profile View All Posts By User
DDTea
International Hazard
*****




Posts: 950
Registered: 25-2-2003
Location: Freedomland
Member Is Offline

Mood: Degenerate

[*] posted on 12-8-2010 at 21:46


This will be hard to show without pictures, and this nomenclature might be arbitrary, but it should explain what's happening. After the initial reaction between dichlorocarbene and cyclopentene, a bicyclic compound is formed--a fused cyclopentane/cyclopropane. Let's call the two shared carbons 1 and 6 and the third member of the cyclopropane ring carbon 2 (I'm doing it this way because these will be their numbers in the resulting cyclohexene ring).

Cyclopropanes are very high energy species; they have a lot of ring strain, which is going to drive this mechanism. So, with that in mind, the electrons between carbons 1 and 6 attack carbon 2, displacing a chloride. The chloride takes its electrons and shifts to carbon 6--similar to a hydride shift--giving you 1,6-dichloro-1-cyclohexene.

This is a neat mechanism because of the principles involved. You can do some thermodynamic calculations if you want; they'll show you that the product is *much* more favored than the reactants here.

(edited for clarity).


[Edited on 8-13-10 by DDTea]




"In the end the proud scientist or philosopher who cannot be bothered to make his thought accessible has no choice but to retire to the heights in which dwell the Great Misunderstood and the Great Ignored, there to rail in Olympic superiority at the folly of mankind." - Reginald Kapp.
View user's profile View All Posts By User
cheeseandbaloney
Harmless
*




Posts: 21
Registered: 4-4-2008
Member Is Offline


thumbup.gif posted on 12-8-2010 at 22:23


oh wow, I was just overlooking the chloride shifting over a carbon! derp. I knew the ring strain was what drove the reaction but didn't know exactly how to approach the first step. Interestingly enough, after building this reaction using a molecular model kit it made a lot more sense in 3d, especially for the double bond reformation. Thanks for the help!

edit: hope this picture works

[Edited on 8/13/2010 by cheeseandbaloney]

reaction.png - 1kB
View user's profile View All Posts By User
Arrhenius
National Hazard
****




Posts: 282
Registered: 17-8-2008
Location: US & A
Member Is Offline

Mood: Stochastic

[*] posted on 13-8-2010 at 00:45


If you enjoy pondering or working through organic mechanisms I would suggest buying "The Art of Writing Reasonable Organic Reaction Mechanisms" by Robert Grossman. This is essentially the standard for mechanistic formality.

The ring expansion you've described is probably not as simple as DDTea described. If you were to draw a mechanism showing the C-Cl sigma bond breaking, populating the sigma* antibonding orbital of the cyclopropyl C-C bond and opening the ring this would not be correct - strictly speaking. In heterolytic mechanisms (moving electron pairs only - not radicals) bond cleavage - think SN2 type 'backside attack' mechanism - results from adding electron density to the antibonding orbital at the atom undergoing the bond forming/breaking event. Frontier orbitals would not predict good overlap for this process to take place. Also, keep in mind that the ring expansion you described might take place under various conditions, and each might utilize a unique mechanism.

Cyclopropanes undergo a rich diversity of reactions, many of which can be best rationalized by homolytic mechanisms. Solvolysis or thermolysis of 6,6-dichlorobicyclo[3.1.0]hexane is probably a radical mechanism, as evidenced by deuterium labeling experiments that show incorporation of deuterium at carbons 1 and 5 of the starting bicycle. The base induced ring expansion is probably best explained by an ionic mechanism (see below), but do not think of this as a 'chloride migration', because the chloride is probably not delivered intramolecularly.


untitled.gif - 19kB
View user's profile View All Posts By User
cheeseandbaloney
Harmless
*




Posts: 21
Registered: 4-4-2008
Member Is Offline


[*] posted on 13-8-2010 at 01:16


Quote: Originally posted by Arrhenius  
If you enjoy pondering or working through organic mechanisms I would suggest buying "The Art of Writing Reasonable Organic Reaction Mechanisms" by Robert Grossman. This is essentially the standard for mechanistic formality.


It's funny you mention that book, because I recently purchased it out of this curiosity. I recently have started teaching myself MO theory and have slowly but surely begun to understand it after drawing and building myself some molecular orbital diagrams. Like visualizing when electron orbitals are 'out of phase' and are antibonding...etc. And I do understand that the conditions present can change the mechanism, (for example, in the case of acid and base hydrolysis, the hydroxide ion is not considered a catalyst, but a reagent therefore it 'promotes' the reaction and is not reversible. Whereas acid hydrolysis is reversible). Things like this.

Admittedly I'm still a little rusty, so Grossman's book gets a little too advanced for me towards the middle, but we all gotta start somewhere, right?

edit: oh! and thanks for the responses so far! Arrhenius, your pictures really puts a lot of the pieces in my head together visualizing the p orbitals like that. Reading can only help me grasp it to a certain degree before I have one of those "a ha!" moments haha

[Edited on 8/13/2010 by cheeseandbaloney]
View user's profile View All Posts By User
DJF90
International Hazard
*****




Posts: 2165
Registered: 15-12-2007
Location: At the bench
Member Is Offline


[*] posted on 13-8-2010 at 03:17


There are several valuable resources out there to help teach organic chemistry. Starting with the most easily accessible, "The virtual organic chemistry textbook" courtesy of MSU is very helpful and is indeed what I started with before I got to university. It often covers mechanisms well, and shows a diverse (but by no means comprehensive) range of chemistry.

http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/intr...

Secondly is a book written by Peter Sykes: "A guidebook to mechanisms in organic chemistry". You can find this online as a free download if you wish. It covers key mechanistic considerations ideal for starting out.

Thirdly is a book you're bound to have seen mentioned before: "Organic Chemistry" by Clayden, Greeves, Warren and Wothers. Again, available for free download if you so wish. Core organic textbook at many universities, covers a broad range of material in significant detail, although it doesn't quite cut it for specialist topics.

Finally, "Designing Organic Syntheses; The disconnection approach", by Stuart Warren. This complements the above book and teaches ways to design synthetic routes. Very much recommended!

As a personal note, bear in mind that not every reaction has its mechanism elucidated. There are many reactions where we're just not sure how the transformation occurs. Similarly, there are reactions where several mechanisms have been postulated, and each holds its own merits. Try not to get hung up on not knowing the mechanism in these cases, as I have done myself before. You just have to accept thats the way it is.

Welcome to sciencemadness, and good luck with your endeavours.
View user's profile View All Posts By User
DDTea
International Hazard
*****




Posts: 950
Registered: 25-2-2003
Location: Freedomland
Member Is Offline

Mood: Degenerate

[*] posted on 13-8-2010 at 04:27


Arrhenius: nice call about the orbital geometry, I didn't think about that.


I'm trying to wrap my head around how this would affect the mechanism, but I can't quite see it: it's worth bearing in mind that in cyclopropane-type systems, the electron density is not concentrated between the atoms as one would expect from a normal sigma bond. There is a lot more pi character at play, so the electron density is concentrated outside of the ring, with the bonding orbitals arranged to form a hexagon rather than a triangle (i.e., imagine the nodes tangent to each vertex of the triangle). If you wanted to explain the type of orbitals in terms of valence-bond theory, you'd have to call them sp4 orbitals, which makes people uncomfortable :) This is confirmed by X-Ray Diffraction.

Here's another proposed mechanism: suppose the bond between the shared carbons breaks, moving to the bridging carbon and displacing a chloride. The result is a six-membered ring carbocation intermediate with charge delocalization. The expelled chloride ion can now bind to either of the two originally shared carbons. This would lead to a racemic product.


DJF90--interesting that you mention "Designing Organic Syntheses; the disconnection approach." I worked with a professor briefly a few years back who studied at Oxford. The two books he told me to look into as soon as possible were that one as well as "The Art of Writing Reasonable Organic Reaction Mechanisms." I never did buy them, though, as my interests shifted away from synthesis.

My turn to recommend a book: Anslyn & Dougherty's "Modern Physical Organic Chemistry." It's probably the best textbook I've ever come across. It's pricey for the amateur, but if you're serious about Organic Chemistry, it's well worth the money. There's more information in that book than you may ever need in your life.

Oh, and Arrhenius--what software did you use to draw your diagram?

[Edited on 8-13-10 by DDTea]




"In the end the proud scientist or philosopher who cannot be bothered to make his thought accessible has no choice but to retire to the heights in which dwell the Great Misunderstood and the Great Ignored, there to rail in Olympic superiority at the folly of mankind." - Reginald Kapp.
View user's profile View All Posts By User
Ozone
International Hazard
*****




Posts: 1210
Registered: 28-7-2005
Location: Good Olde USA
Member Is Offline

Mood: Integrated

[*] posted on 13-8-2010 at 06:47


I recommend:

http://www.amazon.com/Electron-Flow-Organic-Chemistry-Scudde...

Followed by:

http://www.amazon.com/Arrow-Pushing-Organic-Chemistry-Unders...

Cheers,

O3




-Anyone who never made a mistake never tried anything new.
--Albert Einstein
View user's profile View All Posts By User
Arrhenius
National Hazard
****




Posts: 282
Registered: 17-8-2008
Location: US & A
Member Is Offline

Mood: Stochastic

[*] posted on 13-8-2010 at 10:39


cheeseandbaloney: Note that the orbitals I've drawn are SP3 hybrid orbitals, which are not to be confused with P orbitals. There's a simple pneumonic LCAOMO - Linear Combinations of Atomic Orbitals give Molecular Orbitals. This idea gives rise to hybridized SP orbitals that are drawn with a large 'lobe' and small 'lobe' of the dumbbell. While the smaller lobe is not technically the sigma* orbital, it is simple to visualize the sigma C-Cl (grey big lobe) interacting out of phase with what is geometrically analogous to the sigma*C-C (white small lobe). Intuitively, an SP orbital is an S and a P orbital added together (not entirely this simple). In phase interaction of two bonding MO's (molecular orbitals) gives rise to a bond - as I've drawn in for two carbons of the cyclopropane above.

DDTea: Program is Chemdraw. I suggest you download ACD Labs' Chemsketch - free for 'student' version.

For those interested in molecular orbital theory and frontier orbitals I would suggest "Frontier Orbitals and Organic Chemical Reactions" by Ian Fleming

While I agree with DJF90, mechanisms are only our best guess given the information at hand, I would argue that a very strong understanding of mechanism is absolutely crucial if you wish to be an advanced organic chemist. It becomes much easier to predict reactivity or to design transformations - which may or may not be known - and to optimize reaction conditions when you have some idea of how the reaction is taking place. For instance, say you're doing a Mitsunobu Reaction and you observe a large amount of a product containing an alkene instead of the inverted alcohol. Realizing that this arises from elimination of the intermediate oxophosphonium ion might lead you to the idea of adding the azodicarboxylate very slowly so that the concentration of this reactive intermediate is very low compared to the nucleophile.


[Edited on 13-8-2010 by Arrhenius]
View user's profile View All Posts By User
cheeseandbaloney
Harmless
*




Posts: 21
Registered: 4-4-2008
Member Is Offline


[*] posted on 13-8-2010 at 20:28


Thanks Arrhenius, and everybody! I feel I basically mastered everything in orgo 1 in my opinion, with resonance being one of the most important IMO. I've been independently studying organic chemistry for the past 3 years or so simply out of a need to learn it for some reason. I don't plan on going to a university for chemistry, just keeps me sane when I'm bored. Never did well in a school environment anyways.

But! I've gotten to the point where I want to be able to predict reaction mechanisms to reactions I've never seen before. It wasn't till recently that I realized I will hafta master MO theory before I can be more comfortable with doing this (it sure helped me visualize why a diels-alder reaction happens!). Might there be any simple rules to know when a C-C sigma bond will be broken? or hell, I guess if anybody wants to present me with some problems they feel will help further my knowledge, by all means!

DJF90

I actually own "Organic Chemistry" by Clayden, Greeves, Warren and Wothers, but the book I primarily taught myself with was "Organic Chemistry" by Paula Yurkanis Bruice before the other book was recommended to me. I feel books are a great investment, so keep up the suggestions!

edit:
03

I am considering buying one of the two books you suggested since I do not have either. Which of the two would you feel would situate me better for the time being?


[Edited on 8/14/2010 by cheeseandbaloney]
View user's profile View All Posts By User
Arrhenius
National Hazard
****




Posts: 282
Registered: 17-8-2008
Location: US & A
Member Is Offline

Mood: Stochastic

[*] posted on 14-8-2010 at 09:17


There is no simple answer as to when a sigma bond will be broken. Certainly we can think that when a bond breaking event leads to a more stable product, this 'downhill' process is likely to take place. Conversely, we can put energy into a system (heat usually) to drive the reaction 'uphill' on a reaction coordinate. Typically it is extremely difficult to break a sigma bond that is not weakened or strained in some way that will drive its breaking. In your example above, relief of the ring strain associated with a cyclopropane is the driving force. In an SN2 reaction the weak bond to the leaving group is broken to form a stronger bond (but not always stronger). For instance, the Finkelstein reaction forms a weaker bond, but the driving force in this reaction is entropy not enthalpy! This is the case in several other common reactions. The Fischer esterification typically is very poorly favored enthalpically, but clearly can be driven to completion by entropically removing the water by azeotropic distillation or by using a large amount of sulfuric acid to desiccate the reaction.

Other reactions include pericyclic reactions, sigmatropic reactions, metathesis, transition metal catalyzed reactions, photochemical reactions. The list is long. You will probably not become so talented at mechanisms that you will be able to avoid having to learn the enormous number of reactions that are possible. It's easiest to solve mechanistic problems when they look familiar to a reaction you know - at least to have a better idea of when bond formation/cleavage is likely to be allowed.

Here as some relatively simple mechanism problems:


untitled2.bmp - 667kB
View user's profile View All Posts By User
Sandmeyer
International Hazard
*****




Posts: 784
Registered: 9-1-2005
Location: Internet
Member Is Offline

Mood: abbastanza bene

[*] posted on 14-8-2010 at 10:19


Interesting posts Arrhenius! :)

Quote:
While I agree with DJF90, mechanisms are only our best guess given the information at hand


Ideally, organic chemistry should be absolutely analytical, but it would mean that we are able to grasp the infinity. It is empirical, I guess for the same reason that we can not calculate pi. Experiment and extrapolation is the only means the organic chemists (humans) currrently have - in contrast to "God" (and possibly R. B. Woodward :D ).




View user's profile View All Posts By User
kmno4
International Hazard
*****




Posts: 1303
Registered: 1-6-2005
Location: Silly, stupid country
Member Is Offline


[*] posted on 14-8-2010 at 12:22


At first - I am the last one who will propose any mechanisms just out of my head.
"While I agree with DJF90, mechanisms are only our best guess given the information at hand, I would argue that a very strong understanding of mechanism is absolutely crucial if you wish to be an advanced organic chemist."
I cannot agree with it. Guessing means and gives nothing. Reactions go (or not) without our guessing.
Only studying many experimental results can give you right to propose any mechanisms. Of course, some reactions are easy to explain, some are not.
"Very strong understanding of mechanism" is not the same as "very strong ability for writing nicely looking combination of arrows and lines". I have always felt respect for chemical reactions. The more I learn, the deeper respect I feel :D

Back to the point.
Uncatalysed, thermal ring expansion of mentioned gem-dichlorocyclopropane derivative goes most probably via concerted, disrotatory, electrocyclic ring opening at the
C-C bond and a concomitant ionization of a carbon-halogen bond
.
Five-membered ring is itself strained and such isomerisation goes in temperature below 200 C (with 100% yield). In contrast, 6- and 7-membered rings are stable upon reflux above 200 C.

These wisdoms come from review article (one of many about cyclopropanes):
http://dx.doi.org/10.1021/cr0100087
and from literature cited there.
View user's profile View All Posts By User
cheeseandbaloney
Harmless
*




Posts: 21
Registered: 4-4-2008
Member Is Offline


[*] posted on 14-8-2010 at 13:06


Quote: Originally posted by kmno4  

"Very strong understanding of mechanism" is not the same as "very strong ability for writing nicely looking combination of arrows and lines". I have always felt respect for chemical reactions. The more I learn, the deeper respect I feel :D



I couldn't agree more with this statement, although I'm not sure how much weight my opinion holds since I am not a formally trained organic chemist. Although mastering certain mechanisms and why they happen genuinely give me a deeper understanding of manipulating the world on a quantum scale. Pretty arrows and lines only tell part of the story, but if I know why I'm drawing these pretty arrows to point where all those crazy dancing electrons are going, it helps me grasp how molecules bond and break a lot better.

Arrhenius

Thanks for the problems, still goofing around with the last one, but now I have something to do when I get off work. It's kinda funny, figuring out mechanisms is my version of sudoku in a way...
View user's profile View All Posts By User
DJF90
International Hazard
*****




Posts: 2165
Registered: 15-12-2007
Location: At the bench
Member Is Offline


[*] posted on 14-8-2010 at 16:24


Arrhenius: The last reaction you depict, is the base in excess? And 1 eq. MsCl? The only thing I can come up with at this hour is enolate formation, micheal addition to the ethyl acrylate, followed by "displacement" of the tosylate. As a weak base is used, the thermodynamic endo product is obtained. Displacement of the tosylate would of course not be Sn2, but via the carboxonium ion, present because of the anomeric effect.

kmno4: 5 membered rings are actually not all that strained at all. Whoever taught you that should be shot. If a 5 or 6 membered ring can form, it most likely will.

[Edited on 15-8-2010 by DJF90]
View user's profile View All Posts By User
Arrhenius
National Hazard
****




Posts: 282
Registered: 17-8-2008
Location: US & A
Member Is Offline

Mood: Stochastic

[*] posted on 14-8-2010 at 17:00


Haha. I had a feeling folks wouldn't see eye to eye on the importance of mechanism. I absolutely agree that mechanisms can be aggravating at times, because they're abstract and not capable of being proven. Nonetheless, I honestly feel it's important to understand them if you wish to build complex molecules, be it with existing methodology or not.

KMnO4
Quote:

Guessing means and gives nothing. Reactions go (or not) without our guessing.

Perhaps I chose my words poorly. Many reactions are very well established by experimental methods. I don't know how familiar you are with labelling studies, kinetic isotope effects, ultrafast spectroscopy, etc. but people work extremely hard to come close to proving mechanisms, and my hat's off to them (not my cup of tea!). I'll try to dig up some truly astonishing mechanisms - ones that are necessary to rationalize the result of a reaction. As for rationalizing how to make a reaction go, I think the Swern Oxidation is an excellent example. I'm sorry, but one wouldn't come up with the correct series of reagent additions to make that reaction go. I'm near certain that the mechanism preceded that reaction.

DJF90 IIRC there was 3eq of base and ~1eq MsCl. :D Enjoy! Let me know if you get stuck, or if anyone wants the answers. I think there's one excellent answer, and one somewhat acceptable answer for the last one (DJF90's). And yes, I second that - 5 & 6 member rings are not strained.

Ring strain:
3: -27kcal/mol
4: -26kcal/mol
5: 6kcal/mol
6: 0kcal/mol

[Edited on 15-8-2010 by Arrhenius]
View user's profile View All Posts By User
Arrhenius
National Hazard
****




Posts: 282
Registered: 17-8-2008
Location: US & A
Member Is Offline

Mood: Stochastic

[*] posted on 14-8-2010 at 17:18


Here KMnO4, this one's for you:

untitled.gif - 4kB

Not a really astonishing one, but I think you all can solve this one.
View user's profile View All Posts By User
DDTea
International Hazard
*****




Posts: 950
Registered: 25-2-2003
Location: Freedomland
Member Is Offline

Mood: Degenerate

[*] posted on 14-8-2010 at 18:51


Quote: Originally posted by Arrhenius  

Many reactions are very well established by experimental methods. I don't know how familiar you are with labelling studies, kinetic isotope effects, ultrafast spectroscopy, etc. but people work extremely hard to come close to proving mechanisms, and my hat's off to them (not my cup of tea!).



...and for those interested in experimental methods of "proving" mechanisms (or at least lending support to one route over another), Anslyn & Dougherty's "Modern Physical Chemistry" excels here. There are several chapters devoted to kinetic isotope effects and linear free energy relationships.

If you want to see a fanatical love of data, look up some of the papers by C. Gardner Swain.

[Edited on 8-15-10 by DDTea]

[Edited on 8-15-10 by DDTea]

Edit by Nicodem: Fixed the missing "]" which caused a serious formating error.

[Edited on 11/4/2012 by Nicodem]




"In the end the proud scientist or philosopher who cannot be bothered to make his thought accessible has no choice but to retire to the heights in which dwell the Great Misunderstood and the Great Ignored, there to rail in Olympic superiority at the folly of mankind." - Reginald Kapp.
View user's profile View All Posts By User
DJF90
International Hazard
*****




Posts: 2165
Registered: 15-12-2007
Location: At the bench
Member Is Offline


[*] posted on 15-8-2010 at 09:10


Quote:
I think there's one excellent answer, and one somewhat acceptable answer for the last one (DJF90's).


Fire away with the excellent answer...
View user's profile View All Posts By User
Arrhenius
National Hazard
****




Posts: 282
Registered: 17-8-2008
Location: US & A
Member Is Offline

Mood: Stochastic

[*] posted on 15-8-2010 at 14:14


Here are my answers. In #4, the oxidopyrillium species is a well known in dipolar cycloaddition chemistry, hence I've drawn a concerted mechanism. The HOMO-LUMO pairing of the dipole and dipolarophile are such that it gives the 'conjugate addition' product.

answer 1.gif - 13kB

answer 2.gif - 16kB
View user's profile View All Posts By User
Nicodem
Super Moderator
*******




Posts: 4207
Registered: 28-12-2004
Member Is Offline


[*] posted on 15-8-2010 at 14:44


I apologize to drop in this interesting discussion with a banal and off topic request, but Arrhenius, could you provide the reference for that presumable Claisen rearrangement of the allyl hydrazone you gave as an example a couple of posts above. It looks such a useful and ingenious reaction that I would like to read more about it.

To keep on the topic, I would like to stress that mechanism in chemistry is the interpretation of experience itself (like all theory is). It explains the route from A to B and why it does not give C instead. Therefore, without understanding mechanisms it is near to impossible to design a synthesis of more complex structures, let alone optimizing it. For example, if you try to rely on thermodynamics in organic synthesis you get nowhere, but if you combine everything, the knowledge of thermodynamics, activation energies (kinetics), the understanding of transition states and mechanisms in general, you are half way to predict the outcome of any reaction. And correctly predicting the outcome of half of experiments is already in the domain of the best synthetic chemists.
What is however important to always have in mind is that there is a difference in "the most likely mechanism" and "the current understanding of the mechanism" of a reaction. The first is just some fancy arrow pushing and the other is a theory based on experimental work. "The most likely mechanism" is a pedagogic approach on how to build a working hypothesis, and I think this is the kind that a few posters above had in mind when comparing it to guessing. I'm afraid that in schools the difference is rarely emphasized, just like the difference in hypothesis and theory in general is rarely thoroughly explained to the students.

Cheeseandbaloney, for beginners I would highly recommend:
Grossman R.B.: The Art of Writing Reasonable Organic Reaction Mechanisms (2ed., Springer, 2007)

It is an excellent book to have in paper (though if you are a poor amateur you can easily download an illegal PDF copy).




…there is a human touch of the cultist “believer” in every theorist that he must struggle against as being unworthy of the scientist. Some of the greatest men of science have publicly repudiated a theory which earlier they hotly defended. In this lies their scientific temper, not in the scientific defense of the theory. - Weston La Barre (Ghost Dance, 1972)

Read the The ScienceMadness Guidelines!
View user's profile View All Posts By User
Arrhenius
National Hazard
****




Posts: 282
Registered: 17-8-2008
Location: US & A
Member Is Offline

Mood: Stochastic

[*] posted on 15-8-2010 at 17:51


Nicodem: It would technically fall under an aza Cope, not Claisen ;) Regardless: Mundal et al "Triflimide-catalysed sigmatropic rearrangement of N-allylhydrazones as an example of a traceless bond construction" Nature Chemistry 2, 294–297 (2010)

Here's the supp. info.

Unfortunately I don't access to this article. I believe there are several related papers.
And thank you for being the first to back my opinion that mechanisms are useful. You make a good point though.
View user's profile View All Posts By User
Nicodem
Super Moderator
*******




Posts: 4207
Registered: 28-12-2004
Member Is Offline


[*] posted on 15-8-2010 at 23:54


Thanks. I don't have access to that paper either, but hopefully someone will post it in References.
Quote: Originally posted by Arrhenius  
It would technically fall under an aza Cope, not Claisen

This is a good example in the discrepancy between named reactions and mechanisms. Since the mechanism of Cope and Claisen rearrangements are identical (except for the O-heteroatom in Claisen), and there are many other such cases, it is sometimes hard to decide how to call something if the only difference is just a formal nature of reagents, conditions, different heteroatoms or other structural peculiarities. There are many reactions with identical mechanisms and different names (some reactions with mechanistically identical pathways have up to 3 or 4 names!). And there are many reactions with identical outcome, but very different mechanisms (and thus different reaction conditions), so you have chemists who mistakenly tend to use the same reaction name on mechanistically different transformations. Then there are also named reactions that actually can proceed trough more than one mechanism, depending on the reaction partners or conditions. It is confusing territory, mostly because reactions were named before enough experience accumulated to properly interpret it.
For example, I still do not get it why in this particular case calling it an aza-Cope would be more appropriate than aza-Claisen, but I guess the authors had their own opinion on this. Perhaps because Claisen rearrangements are an undergroup of Cope rearrangements? But then they use a catalyst that can only catalyse Claisen but not Cope rearrangements (protonation of the heteroatom and the heteroatom is a Claisen's peculiarity).

I noticed during my work that people usually do not comprehend the importance of understanding mechanisms (and all the theory in general) until they start to get more involved in practical lab work, particularly designing syntheses. It then becomes obvious that those who have limited knowledge in mechanisms become very handicapped in their practical experimental work. They tend to rely on asking others for advices on how to perform reactions, with which reagents, what conditions, what protection groups, etc. Usually they become an annoyance to the coworkers, especially when these realize the only reason they ask advice is because they are to lazy to learn mechanisms. Such people also tend to be completely unable to design rational synthetic routes and this is a terrible handicap if your job is to develop target oriented syntheses. Another consequence is in that they tend to become more sensitive to "synthetic frustrations" and as a consequence try to limit their research to a single chemical transformation (though this is only allowed in the academy - in the industry they simply fire you if try that). I worked with few such people and always felt kind of sorry for them, but once they get too old to learn it is too late to repair the situation (I see it on myself - I'm sorry I did not learn more theory when I was younger and the learning process was easier). So my advice to students would be to never give up on learning theory. Not doing so will make you a very unhappy and unsuccessful chemist, possibly unemployed or employed in some office of some governmental agency. Theory is after all practice condensed in knowledge, so you can not do without it if you have to do practical work.




…there is a human touch of the cultist “believer” in every theorist that he must struggle against as being unworthy of the scientist. Some of the greatest men of science have publicly repudiated a theory which earlier they hotly defended. In this lies their scientific temper, not in the scientific defense of the theory. - Weston La Barre (Ghost Dance, 1972)

Read the The ScienceMadness Guidelines!
View user's profile View All Posts By User
Sandmeyer
International Hazard
*****




Posts: 784
Registered: 9-1-2005
Location: Internet
Member Is Offline

Mood: abbastanza bene

[*] posted on 16-8-2010 at 09:52


Quote: Originally posted by Nicodem  
For example, I still do not get it why in this particular case calling it an aza-Cope would be more appropriate than aza-Claisen, but I guess the authors had their own opinion on this. Perhaps because Claisen rearrangements are an undergroup of Cope rearrangements? But then they use a catalyst that can only catalyse Claisen but not Cope rearrangements (protonation of the heteroatom and the heteroatom is a Claisen's peculiarity).


If we compare the products, namely 1,5-dienes, resulting from both Cope and Claisen rearrangements we see that in the 1,5-diene-product from Claisen, one double bond is always a C=O, that is not the case with Cope rearrangements. So, I would say that Arrhenius is right, it should be called aza-Cope, if the above example would be a aza-Claisen, as you claim, it would contain one carbonyl group as one "ene" of the 1,5-diene. As far as the catalyst goes, we can also see it as if they just shown that Cope rearrangement can also be catalysed by the same catalyst as Claisen. Many different reactions can be catalysed by the same catalyst, for example we don't change the name of Diels-Alder reaction into Friedel-Crafts just because a Lewis acid can catalyse it.




View user's profile View All Posts By User
un0me2
aliced25 sock puppet
***




Posts: 205
Registered: 3-2-2010
Member Is Offline


[*] posted on 16-8-2010 at 13:53


Quote: Originally posted by Arrhenius  
....

DDTea: Program is Chemdraw. I suggest you download ACD Labs' Chemsketch - free for 'student' version.

.......


There is a better "FREE" program available, No-Fee, Symyx Draw for Students/Academics & Home Use (http://www.symyx.com/micro/getdraw/). You have to register to download it, but it kicks shit out of Chemsketch (which always gives funky as hell structures when you press F9). It also has an export as picture function.




quam temere in nosmet legem sancimus iniquam
View user's profile View All Posts By User
 Pages:  1    3  ..  5

  Go To Top